R Markdown test rmd

---

1 read a table; capture prov info

source(file.path(dir_test, 'test_source.R'))

## File `~/github/ohibc/rmd_testing/tableA.csv`: git commit info unavailable.  Not version-controlled in Git?
## File `~/github/ohibc/rmd_testing/tableB.csv`: most recent commit info: commit 00b6e10615d39b60a92958f7d8887c9e1091af54 Author: Casey O'Hara <ohara@nceas.ucsb.edu> Date:   Sat Apr 30 10:25:32 2016 -0700; uncommitted changes = FALSE
## File `~/github/ohibc/rmd_testing/tableC.csv`: most recent commit info: commit 00b6e10615d39b60a92958f7d8887c9e1091af54 Author: Casey O'Hara <ohara@nceas.ucsb.edu> Date:   Sat Apr 30 10:25:32 2016 -0700; uncommitted changes = FALSE
## File `~/github/ohibc/rmd_testing/table1.csv`: most recent commit info: commit 893b6768bfa73aae999c60b5c61cdfd2e501944e Author: Casey O'Hara <ohara@nceas.ucsb.edu> Date:   Fri Nov 13 11:03:56 2015 -0800; uncommitted changes = FALSE
## File `~/github/ohibc/rmd_testing/test_source.R`: git commit info unavailable.  Not version-controlled in Git?

tableA      <- read_csv(tableA_file)

## File `~/github/ohibc/rmd_testing/tableA.csv`: git commit info unavailable.  Not version-controlled in Git?

write_csv(tableA, tableB_file)

## File `~/github/ohibc/rmd_testing/tableB.csv`: most recent commit info: commit 00b6e10615d39b60a92958f7d8887c9e1091af54 Author: Casey O'Hara <ohara@nceas.ucsb.edu> Date:   Sat Apr 30 10:25:32 2016 -0700; uncommitted changes = FALSE

---

2 The next section (below the divider) is the footer, knitted as a child

The code for the R code chunk header looks like this:

{r child = file.path(dir_git, 'src/templates/ohibc_prov_ftr.Rmd')}

Note that it is executed as if it were just part of this main document; it numbers the section (“Provenance”) as a continuation of the numbering, and the variables are evaluated in the environment of the main document.

---

3 Provenance

• Run ID: 23; run tag: “standard run”
• Run elapsed time: 4.942 seconds; run memory usage: NA MB
• System info: System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara.
• Session info
  • R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite).
  • Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base
  • Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3

Provenance summary for run 23: standard run (Sat Apr 30 11:58:56 2016)

file_name	file_dir	filetype	uncomm_chgs	commit_id
table1.csv	/Users/caseyohara/github/ohibc/rmd_testing	input	FALSE	01944e
table1.csv	/Users/caseyohara/github/ohibc/rmd_testing	input	FALSE	01944e
tableA.csv	/Users/caseyohara/github/ohibc/rmd_testing	input	TRUE	NA
tableA.csv	/Users/caseyohara/github/ohibc/rmd_testing	input	TRUE	NA
table2.csv	/Users/caseyohara/github/ohibc/rmd_testing	output	FALSE	91af54
table2.csv	/Users/caseyohara/github/ohibc/rmd_testing	output	FALSE	91af54
table3.csv	/Users/caseyohara/github/ohibc/rmd_testing	output	FALSE	91af54
tableB.csv	/Users/caseyohara/github/ohibc/rmd_testing	output	FALSE	91af54
tableB.csv	/Users/caseyohara/github/ohibc/rmd_testing	output	FALSE	91af54
tableC.csv	/Users/caseyohara/github/ohibc/rmd_testing	output	FALSE	91af54
test.Rmd	/Users/caseyohara/github/ohibc/rmd_testing	script	TRUE	17eb33
test_source.R	/Users/caseyohara/github/ohibc/rmd_testing	sourced_script	TRUE	NA